Chemical preparation of high specific activity nucleotide probes

ABSTRACT

Methods of chemical synthesis of labeled nucleotide probes are described. The methods comprise providing a first target recognition moiety comprising a nucleotide sequence of at least about 15 nucleotide bases including at least one 5&#39; end and 3&#39; end. The first target recognition moiety is chemically altered to contain a carboxyl group. A second signal generating moiety comprising a hydroxyl group is provided. The carboxyl group of the first target recognition moiety is chemically reacted with hydroxyl group of the second signal generating moiety to chemically join the two moieties and produce said labeled nucleotide probe.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a division of application Ser. No. 08,142,232 filedOct. 25, 1993, which is U.S. Pat. No. 5,521,298 issued May 28, 1996,which is a continuation of application Ser. No. 07/285,274, filed Dec.16, 1988, which is U.S. Pat. No. 5,324,829 issued Jun. 28, 1994.

BACKGROUND OF THE INVENTION

Specific oligonucleotide sequences are very useful tools in detectingcomplementary nucleotide sequences. The two requirements of the nucleicacid probe are a sequence specific signal and the formation of elementswhich will convert single hybridization events into multiple detectableevents. In current enzymatic methods for preparing labeled probes,radioactive or biotinylated nucleotides are introduced into the probesby the use of polymerizing enzymes like DNA polymerase or terminaltransferase. Methods are also available for introducing single enzymesor hapten molecules into DNA chemically, but these singly tagged probesdo not generate enough signal, thus lacking the sensitivity needed fordetecting complementary sequences in biological samples.

For example, Ward et al. in U.S. Pat. No. 4,711,955, discloses aprocedure for derivatizing nucleotides with chemical determinants. Thederivatized nucleotides are then enzymatically polymerized. Thus, theseanalogs function as substrates for nucleic acid polymerases. For thispurpose, it is crucial that the chemical determinants not be placed onring positions that sterically, or otherwise, interfere with normalWatson Crick hydrogen bonding potential of the bases.

SUMMARY OF THE INVENTION

The present invention provides an alternative to the syntheses oflabeled nucleic acid probes known to the art. The procedure disclosedherein is a chemical synthesis of a labeled "nucleotide probe" whichcomprises the steps of:

a) providing a first "target recognition moiety" comprising a nucleotidesequence of at least about 10 nucleotide bases, said sequence containingat least one "5' end" and "3' end",

b) chemically altering said first target recognition moiety to contain a"reactive functionality" at said 5' end or said 3' end, or both, and

c) providing a second "signal generating moiety", having at least oneterminus containing a functionality capable of reacting with at leastone reactive functionality provided on said first target recognitionmoiety, and

d) chemically reacting said first target recognition moiety, nowcontaining at least one reactive functionality, with said at least oneterminus of said second signal generating moiety, to chemically jointhese two moieties and produce said labeled nucleotide probe.

In some embodiments, one or both termini of the signal generating moietyare chemically modified to contain a functionality that will react withone or both of the reactive functionalities of the target recognitionmoiety.

The present invention also provides labeled nucleotide probes formedfrom this chemical joinder of the two components, and diagnostic andresearch reagents containing said probes.

As used herein, the term "nucleotide probe" means a labeled nucleotidesequence having as part of that sequence, a moiety that can hybridize,at least in part, to an analyte nucleotide sequence, and can be usefulto detect, monitor, localize, isolate and the like, said analytesequence. The term should be interpreted broadly to includeoligonucleotides, homopolynucleotides, polynucleotides and the like.

As used herein, it is understood that "hybridization" refers tocomplementary base pair binding to all or a portion of a target nucleicacid sequence, i.e: the probes must contain at least somecomplementarity. It should be understood that this binding does not haveto be perfectly matched. There may, in fact, be unpaired regions,resulting in interior loops, bulge loops, hairpin loops, cruciformbinding, or any other mismatched regions. Hybridization need only occurto the extent necessary to allow detection of the target.

As used herein, the term "target recognition moiety" (TRM) means thatpart of the probe that will hybridize or bind to sample analyte. Thetarget recognition moiety comprises a nucleotide sequence and can takeon any suitable configuration for binding to said analyte, whether thatbe a specific sequence of nucleotide bases, a homopolynucleotidesequence, or the like.

As used herein, "signal generating moiety" (SGM) means that part of theprobe that can generate a signal through a radioactive label, enzymaticlabel, chemical label, immunogenic label, and the like.

As used herein, "target analyte sequence" refers to all or a portion ofthe nucleic acid contained in or relating to biological matter that maybe found in a biological, physiological, environmental sample or thelike.

As used herein, "5' end" and "3' end" should be construed as the meaninggenerally accepted in the art, namely, the terminal nucleotide at oneend of a nucleotide sequence which has a free 5' or 3' group, whereinone of the oxygens of the phosphorous is free to join to either thefifth or third carbon atom respectively of a pentose.

Chemical synthesis of the probes as described herein provides advantagesin that a more controlled amount of label is incorporated into thesignal generating moiety. Thus, amplification of signal may be easilyaccomplished. The label may be applied to various positions on thesignal generating moiety, when that moiety is a polynucleotide. Inpreferred embodiments, the signal-generating moiety is a polynucleotideand the label is applied to positions on the polynucleotide that willinterfere with the capability of this nucleotide to hybridize, thusensuring that only the target recognition moiety hybridizes to targetanalyte. Not only does the signal generating moiety not have to beavailable for nucleic acid hybridization, in some embodiments, thesignal generating moiety may even comprise polymers other thanpolynucleotides, and therefore couldn't be available to hybridize.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a schematic representation of one embodiment of the inventionwherein the target recognition moiety is modified to contain at leastone terminal carboxyl functionality, and then reacted with signalgenerating moiety via an ester linkage, to form a nucleotide probe.

FIG. 2 is a schematic representation of a second embodiment of themethod of the invention wherein the target recognition moiety isprovided with at least one terminal amino functionality for formation ofa phosphoamide linkage with signal generating moiety, to form anucleotide probe.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides a procedure for chemical synthesis of alabeled nucleotide probe by a chemical coupling or joinder of the twocomponents of the probe, namely the target recognition sequence moietyand the signal generating moiety.

The first component of the labeled nucleotide probes of the invention isthe target recognition sequence moiety, which comprises a nucleotidesequence of at least about 10 nucleotide bases. This moiety is capableof hybridizing in whole or in part to target analyte. It may be providedin any of a variety of ways. For example, it may be isolated from thegenomic DNA of an organism it is desired to detect, it may berecombinantly produced, or it may be chemically synthesized by standardoligonucleotide synthesis procedures. A good description of suchsuitable procedures for the latter may be found in Methods inEnzymology, Volume 154, pages 221-328, Academic Press N.J. 1987, Ray Wuand L. Grossman, editors. Any configuration of nitrogenous bases,including adenine, guanine, cytosine, thymine, uracil, ormethylcytosine, are contemplated to form the nucleotide sequence of thismoiety, as long as the moiety is capable of binding, at least to someextent, with at least a portion of the nucleic acid of an analyte.

The binding event is any complementary base pair binding to an extentsuitable to allow detection of the target analyte. In this regard then,the length of the nucleotide sequence of the target recognition moietymay also vary widely, ranging from several hundred bases to less thanabout 100 bases, and preferably about 5-75, more preferably about 5-60,and most preferably about 15-50 bases. At this time, these lattersequence lengths are preferred in that it has been found that thislength affords ease of use. This is generally due to the phenomenon thatsequences in the range of 15 to 50 nucleotide bases are easy tosynthesize conveniently, and cost effectively, and have enough hydrogenbonding capability to give stable double-stranded structure to survivevarious manipulations and treatments. Sequences of greater than about100 bases can pose difficulty during use in that they are more difficultto synthesize, less cost effective and increase the chances of fosteringintramolecular secondary structures. It is well known that beyond acertain length of polynucleotide sequence, very little additionalstability would be imparted to the hybrids. One skilled in the art willappreciate that a suitable sequence length for this binding moiety willalso be governed to some extent by the binding characteristics of theanalyte sequence itself.

It should be appreciated that in some instances it may be desirable toincorporate derivatives or other chemical moieties at various positionsin the nucleotide sequence of the target recognition moiety, for avariety of reasons such as to serve as reporter molecules directly orindirectly. For example, derivatives such as 5 substituted pyrimidineand 7 substituted purine may be desired. Any such derivatives are withinthe contemplation of the invention, as long as the addition of suchchemical derivatives to various positions in the sequence does notinterfere substantially with binding of target recognition moiety toanalyte.

The second component of the probes is the signal generating moiety. Thiscomprises any polymer that is capable of containing a detectable label,and is further capable of chemical linkage to the target recognitionmoiety, by virtue of a functional group on at least one terminus.Illustrative of suitable polymers in this regard are proteins, such asalbumin and gelatin, derivatized latex beads, dextrans, other syntheticor natural biopolymers, and nucleotides, including homopolynucleotides,oligonucleotides, and the like. Preferred among these polymers for usein the signal generating moiety, are nucleotide sequences. This may beattributed to their ease of synthesis and labeling, and controllableamplification. These nucleotide sequences may vary widely in theirspecific sequence, as long as they contain label which is capable ofsignaling the binding of the target recognition moiety portion of theprobe to analyte. The nucleotide sequences may be DNA or RNA. One of themajor advantages afforded by the preferred signal generating moiety, thepolynucleotide sequence, is the ability for the user to provide multiplelabels at defined places in the sequence. This affords more user controlthen was previously possible. The labeling of the polymer in the signalgenerating moiety may take on many forms, including conventionalradioisotopic labeling, chemical labeling, immunogenic labeling, or alabel with light scattering affect, and the like.

Thus, the label of the signal generating moiety may comprise aradiolabel (e.g. ¹⁴ C, ³² P, ³ H, and the like), an enzyme (e.g.,peroxidase, alkaline or acid phosphatase, and the like), a bacteriallabel, a fluorescent label, an antibody (which may be used in a doubleantibody system), an antigen (to be used with a labeled antibody), asmall molecule such as a hapten like biotin (to be used with an avidin,streptavidin, or antibiotin system), a hapten such as fluorescein to beused with an anti-fluorescein, a latex particle (to be used in abuoyancy or latex agglutination system), an electron dense compound suchas ferritin (to be used with electron microscopy), or a light scatteringparticle such as colloidal gold, or any combinations or permutationsthereof.

Signal is generated by the signal generating moiety in any variety ofconventional techniques. For example, if the label portion of the signalgenerating moiety is an antigen, a signal can be generated by complexingsaid antigen with an antibody/enzyme conjugate, followed by addition ofenzyme substrate. If the labeling portion of the signal generatingmoiety is an antibody, signal can be generated by complexinganti-antibody or an F_(c) binding protein such as Protein A therewith,which second antibody or Protein A has already been conjugated to anenzyme.

For reasons of ease and safety in the handling of the probe, it ispreferred that the signal generating moiety be chemically labeled,especially immunogenically or enzymatically. In more preferredembodiments, the chemical label of choice is a hapten, such as biotin,iminobiotin, fluorescein, and the like. These are preferred at thepresent time due to ease of synthesis, as well as the availability ofhigh specific activity secondary reagents and techniques for using them.For example, the signal generating moiety may be labeled with a haptenthrough conventional techniques such as treatment with an alkyldiamine.Activated haptens such as biotin-NHS ester, fluorescein isothiocyanate(FITC), and the like may be chemically attached through the aminofunctionalities. In this manner, the amount of activated hapten presentis controlled by the availability of the amino functionalities providedby the user for this purpose, by the treatment with the alkyldiamine.

In one preferred embodiment wherein the signal generating moietycomprises a nucleotide sequence, the signal generating moiety generatessignal based on the biotin/streptavidin system. This system can beincorporated into the signal generating moiety by a variety of means.For example, the nucleotide portion of the signal generating moiety canbe covalently attached to biotin via a cytochrome c bridge (Manning etal, Biochemistry, 16: 1364-1370 (1977), Manning et al, Chromosoma, 53:107-117 (1975), Sodja, A., Nucleic Acids Research, 5: 385-401 (1978)),or the biotin can be covalently incorporated into specific nucleotideresidues (Langer, P. R., Proceedings of one National Academy ofSciences, USA, 78: 6633-6637 (1981), or, as alluded to above, the biotincan be attached to a polynucleotide by means of a diamine (e.g., pentanediamine) bridge (Broker, T. R., et al, Nucleic Acids Research 3: 363-384(1978)). Interaction of the biotin molecules in the signal generatingmoiety with avidin, streptavidin or antibiotin antibodies is thencarried out, wherein the avidin, streptavidin or the antibodies areconjugated to such signalling components as latex particles (Sodja, A.,et al, supra, or Manning. et al Chromosoma, supra), ferritin (Broker,supra), a fluorogen such as fluorescein, an enzyme, secondaryantibodies, magnetic particles, or the like.

It should also be noted that the function of the signal generatingmoiety is to signal the presence of binding to analyte. Hence, it shouldbe appreciated that it is undesirable for nucleotides within this moietyto hybridize to analyte, or any other bases that may be present in asample under analysis, as this may quench any signal to be generated.Therefore, it is preferable to substitute the cytosine bases on thefourth carbon atom with a hapten such as biotin, immunobiotin,fluorescein, or the like, to prevent this base's normal hybridizationfunction.

The signal generating moiety may be obtained commercially or preparedfrom any appropriate source, including denatured single-stranded DNAfrom natural sources, RNA from material sources, chemical synthesis ofoligonucleotides, polynucleotides, including homopolynucleotides andhomooligonucleotides. This sequence varies in length in a mannercommensurate with the signal amplification required and the amount oflabel it is desired to attach. However, lengths of about 50 to 200 havebeen found to be particularly useful due to the amplification requiredfor the detection of biological samples and the practical limitations ofsynthesizing the long sequence. Also, it should be understood that verylong tails will tend to affect hybridization rates. Preferred lengthsrange from about 50 to about 200, most preferred being about 100 toabout 150.

In the first step of the method of the invention, the 5' or 3' terminusor both of the nucleotide sequence of the target recognition moiety ischemically altered to incorporate a reactive functionality which willallow chemical linkage of this target recognition moiety with one orboth termini of the second component of the probe, the signal generatingmoiety. Suitable functionalities vary widely, but may, in general, bedescribed as those that will allow chemical attachment of the twocomponents either at the 3' end or the 5' end of the target sequence.This chemical attachment of the signal generating moiety to the targetrecognition moiety, forming the probes as described herein, is robust todisassociation of these two moieties in the subsequent use of the probesin hybridization assays. In other words, the two components of the probeshould not detach from each other upon hybridization of the targetsequence moiety of the probe to target analyte. Thus, when the probe ishybridized to target analyte, it will then carry with it, signal moiety,to label this complexation, which label is later detected.

A number of methods can be used to generate a variety of functionalitiesat one or both termini of the target recognition moiety. With theavailability of these reactive functionalities so generated, it shouldbe appreciated that a number of chemistries may be used to then link thetwo components of the probe together. Of the preferred functionalitiesmay be mentioned carboxyl groups, phosphate groups, thiol groups, aminogroups, hydroxyl groups and the like. Of the preferred chemicallinkages, linking one component to the other, may be mentioned esterlinkages, phosphate ester linkages, phosphamide linkages, disulfidelinkages, and the like.

One skilled in the art will readily appreciate that the signalgenerating moiety must also contain an appropriate functionality capableof reacting with the functionality generated at one or both termini ofthe target recognition moiety. Thus, in some instances, if such afunctionality is not already present, an appropriate functionality mustalso be generated at one or both termini of this signal generatingmoiety. The following table depicts illustrative functionalities thatmay be provided at the termini of the target recognition moiety or thesignal generating moiety, and the resulting chemical linkage:

    ______________________________________                                        Target Recognition                                                                         Signal Generating                                                                          Chemical                                            Moiety       Moiety       Linkage                                             ______________________________________                                        1.  phosphate group                                                                            hydroxyl group                                                                             phosphate                                                                     ester linkage                                   2.  carboxyl group                                                                             hydroxyl group                                                                             ester linkage                                   3.  amino group  phosphate group                                                                            phosphoamide linkage                            4.  thiol        sulphydryl   disulfide linkage                               ______________________________________                                    

The above-suggested combinations could be completely reversed withrespect to the functionalities described for each respective moiety. Forexample, the target recognition moiety may contain a terminal hydroxylgroup while the signal generating moiety contains, or is altered tocontain, a phosphate group, and so on.

Referring now to the first illustration in the above table, one or bothtermini of the target recognition moiety is provided with a phosphatefunctionality either through chemical means or through enzymatic means.This may be accomplished through the use of well-known phosphorylationtechniques in the art such as using polynucleotide kinase and ATP orperforming phosphorylation during chemical synthesis, and the like. Thesignal generating moiety may contain a terminal hydroxyl group.Alternatively, it may be modified by well-known phosphorylationprocedures to contain a phosphate group which is then converted to anamine, carboxyl, or thiol group, using conventional chemistry. The twomoieties, now containing appropriate terminal reactive functionalities,are then allowed to react using conventional methods such as couplingwith water soluble carbodiimides, or the linking of the two componentsby the use of heterobifunctional reagents.

Referring now to the second illustrative combination, which reactionscheme is also illustrated by FIG. 1, the target recognition sequence ismodified to contain a carboxyl functionality at one or both termini. Ina preferred embodiment, this may be accomplished by firstphosphorylating either the 3' end or the 5' end. The phosphate group ofthe phosphorylated DNA is then activated with animidazole/ethyl-dimethylamino-propyl carbodiimide (EDAC), and thenreacted with an excess of an amino acid such as ε-amino caproic acid toproduce the carboxyl group. The target recognition moiety is thenreacted with signal generating moiety containing a reactive terminalhydroxyl group in the presence of excess EDAC to form an ester linkage,chemically linking the two moieties.

Referring now to the third permutation, which reaction sequence isfurther illustrated by FIG. 2, a phosphorylated target recognitionmoiety is provided with an amino functionality by reaction of activatedphosphate with a diamine. Preferred is reaction with EDAC as describedabove for the second illustration, and subsequent reaction with anexcess of an alkyldiamine such as hexyldiamine.

In the fourth illustrated combination from the above table, aphosphorylated target recognition moiety is first aminated as describedabove, the amino functionality then being converted to a thiol group bythe use of appropriate heterobifunctional reagents, like N-succinimidyl3-(2-pyridyl dithio) propionate (SPDP). In this combination, one or bothtermini of the signal generating moiety is provided with a sulfhydrylgroup. The two components are then reacted, using oxidative couplings,to form a disulfide linkage, or by the use of a maleimide group on oneend and SH on the other.

As referred to above, the signal generating moiety comprises any polymercapable of containing a detectable label, which polymer is furthercapable of chemical linkage to one or both termini of the targetrecognition moiety. Multifunctional polymers may be suitably used tocomprise this moiety. For example, polymers may be used which containcarboxyl groups for the labeling portions, such as biotin and the like,and also contain at least one terminal amino functionality for chemicallinkage to the target recognition sequence.

Polysaccharides may also be suitably used wherein hydroxyl groups on theterminal monosaccharides are converted to aldehydes which may then reactwith a target recognition moiety containing a terminal aminofunctionality.

Ribonucleotides having a diol group at the 3' end may be similarlymodified by conventional periodate reaction to yield a dialdehyde. Thedialdehyde may then be converted to amino groups by reductive aminationand then reacted with target recognition moiety, forming a phosphoamidelinkage or any other appropriate linkage. Alternatively, the aldehydegroups may be reacted with 5' or 3' amino functionalities provided onthe target recognition moiety, to form a Schiff's Base followed byborohydride reduction. The following depicts these last-mentionedschemes: ##STR1##

As alluded to throughout the text, one or both terminii of either thesignal generating moiety or the target recognition moiety is providedwith a reactive functionality as described herein. If both termini of atarget recognition moiety are reactive, it is conceivable that achemical linkage could be formed at both ends with signal generatingmoiety. The probe would then be constructed with a target recognitionmoiety flanked on either side with signal generating moiety. If bothtermini of the signal generating moiety are reactive, the oppositeconstruct would be formed. If each of the components of the nucleotideprobe have reactive groups provided at either end, then a repetitivepolymer or a cyclic labeled probe could be formed.

In the preferred embodiments, wherein the signal generating moietycomprises nucleotide bases, all possible terminus--terminus combinationsare within the contemplation of the invention. For example, the chemicallinkage may be a 5' to 5' linkage, a 3' to 3' linkage, or a 5' to 3', ora 3' to 5' linkage. Each prospective terminus would be provided in asuitable manner with the functionality capable of reacting with theterminus of the other component.

The nucleotide probe constructed as above may be provided as a reagentsolution, comprising one or more nucleotide probes as described herein,and a buffer. Suitable buffers are generally aqueous and may containdextran sulfate, EDTA, and similar additives, whether present alone orin any combination, provided that the additives are compatible with thesubsequent hybridization of the reagent to target analyte. The reagentsolution may also comprise agents that enhance the ability of the probeto bind to target, such as suitable hybridization enhancers, carrierDNA, and compounds to increase the specificity, such at formamide. Inthis solution format, the shelf-life of the probe reagent generallyranges over a year. Alternatively, the probe may be lyophilized and thusprovided in dry reagent form to be reconstituted with buffers such asthose described above, prior to the user conducting hybridization assayswith sample analyte.

The method and use of the hybridization probe and reagents described bythis invention assumes the prior selection of an analyte targetpolynucleotide sequence. In many embodiments, detection of a particularanalyte will be desired because the particular sequence of purine andpyrimidine bases in the target polynucleotide is known or thought to becharacteristic of a mutated or normal gene of an organism, and becausethe presence or absence of this particular mutated or normal gene can becorrelated with the presence or absence of an infectious agent,carcinogen, disease state, or some other genetic trait.

The use of the probes as described herein is not limited to any specificmethod or technique of conducting hybridization to the nucleic acid in abiological specimen, to detect the target sequence. Severalhybridization assay techniques are known to the art and include, forexample, dot blot hybridization, Southern blotting; sandwichhybridization assays such as those described by Ranki, et al., in U.S.Pat. Nos. 4,563,415 and 4,486,539; sandwich hybridization on beads asdescribed by Hansen, et al. in European Patent Application 84306513.7;displacement hybridization techniques such as those described in WO87/03911; capture techniques wherein the nucleic acid probes asdescribed herein are first immobilized onto a solid support and thencontacted with sample; in situ hybridization such as those cited ordescribed by Ploeg, Folia Histochemica et Cytobiologica, Vol. 24 (1986)No. 3, pp 189-194; and the like.

The target analyte nucleotide sequence may be present in various media,most often in a biological, physiological, or environmental specimen. Itis preferred in some cases to subject the specimen containing the targetanalyte sequence to a variety of extraction, purification, and isolationprotocols before conducting analysis according to the methods of thisinvention. Measures such as these are desirable to rid the sample ofsubstances that might interfere with binding of the analyte to thehybridization probe. Examples of such protocols may be found in thesecond chapter of Nucleic Acid Hybridization, ed. B. Hames & S. Higgins,IRL Press, Washington, D.C. (1985), and in standard textbooks.

It is also within the contemplation of the present invention thatsynthetic homo- or hetero- polynucleotides can be prepared in thelaboratory to serve as the target analyte sequence despite theirabiological origins, as such synthetic polynucleotides are oftendesirable for research purposes and the like.

Notwithstanding the foregoing, it is preferred in some cases that thetarget analyte sequence be in a single-stranded form to facilitatehybridization to the target recognition moiety of the hybridizationprobe formed by the methods of the invention. Sample containing targetanalyte nucleotide sequences must often be treated to convert any targetanalyte to single-stranded form. This conversion to single-stranded formmay be accomplished by a variety of ways conventional to the art. Forexample, the denaturation of duplex nucleic acids can be accomplishedthermally, chemically or in other conventional ways. The denaturationprocess will depend upon the pH, ionic strength, temperature, and otherproperties of the ambient medium (e.g., presence of urea, formamide,glyoxal, methyl mercury hydroxide or other agents), as well as upon thebase composition (i.e., the GC/AT ratio), sequence, and length of theduplex nucleic acid. Reviews of various methods of denaturation may befound in standard textbooks, and in J. Marmur, C. Schildkraut and P.Doty in Molecular Basis of Neoplasia, Univ. of Texas Press, Austin, Tex.1962.

Exemplary of a hybridization reaction are situations wherein the targetanalyte sequence is present in a liquid medium. This medium may takemany forms, most illustrative of which is unprocessed biological fluid.The unprocessed biological fluid can be mixed with a "second solution"in some embodiments so as to produce a medium known to supportrehybridization of complementary single-stranded nucleic acids.

The second solution may be aqueous or nonaqueous or a mixture of both.Certain inorganic or organic additives known to affect rehybridizationof complementary single-stranded nucleic acids may be added to enhancethe rate of hybridization and/or to increase the equilibrium extent ofrehybridization (i.e., stability of the rehybridized form). Of theinorganic additives may be mentioned sodium citrate and sodium chloride;of the organic compounds may be mentioned such compounds as formamide.Other useful additives are polyethylene glycol, dextran sulfate, sodiumdodecyl sulfate and casein.

The probe may be contacted with a liquid sample under conditions inwhich the analyte target sequence, if present, can hybridize in whole orin part to a complementary region contained in the target recognitionmoiety of the nucleotide probe. This contacting step may be effectuatedin a variety of ways, and under varying conditions of "stringency". Areview of factors which affect rehybridization (reassociation) processesis available in Nucleic Acid Hybridization, ed. B. Hames and S. Higgins,IRL Press, Washington, D.C. (1985). The factors include conditions oftemperature, pH, salt concentration and solvent medium, in addition tofactors which reflect the length, complexity, and degree ofcomplementarity of the probe and analyte target polynucleotides. Thecontact period may vary depending on the length of time necessary toeffect hybridization to the desired extent, which is dependent in parton the length of the binding region in the target recognition moiety aswell as the reaction conditions.

The nucleotide probe, with any bound complementary target analytesequence, is separated from the biological sample after the desiredhybridization has taken place. This separation may be accomplished byany suitable procedure including, but not limited to chromatography(column, gel, etc.), filtration, electrophoresis (includingelectroelution) and the like. It may be further desirable to incorporatea rinsing step to ensure that unbound material is fully separated fromrehybridized material which has bound to the probe.

Once the hybridization event has taken place and the bound material isseparated from unbound, detection of the label on the signal generatingmoiety is undertaken by assaying the bound material, unbound material,or both.

If the label is a radioactive one, direct detection can be accomplishedthrough conventional radioisotopic quantitation techniques.

If the label is a chemical one, as for example, biotin, indirectdetection takes place. Examples of this include contact with achromogenic substrate, or the like, well-known to the art.

The following Examples provide more specific embodiments of the presentinvention, but are not to be considered limitative thereof.

EXAMPLES Preparation of Oligomers For Use as Signal-Generating andTarget Recognition Moieties

All oligonucleotides were synthesized by typical phosphoramiditechemistry on a DNA synthesizer using 5 Phosphate-on cyanoethylphosphoramidite after which the oligomer was deblocked to remove theprotecting groups. Alternatively, the phosphate group was added by theaction of polynucleotide kinase (after deblocking). The oligomer waspurified after the synthesis over a column containing dextran gel beadshaving an exclusion volume of about 25,000 daltons (SEPHADEX G 25,Pharmacia, Inc., Piscataway, N.J.).

The signal generating moiety oligomer was synthesized on a DNAsynthesizer and in some cases the capping step after each coupling waseliminated. This oligomer was 50-200 bases in length; with 20-100% ofthe bases being cytosines. After deblocking and then desalting over acolumn containing dextran gel beads having an exclusion volume of about25,000 daltons (SEPHADEX G 25, Pharmacia, Inc., Piscataway, N.J.), theoligomer was lyophilized and the exocyclic amino groups of the C's weretransaminated by adding 2 mls of the transamination mix of the driedoligomer and shaken at room temperature for 24-72 hours. Thetransamination mix was made up as follows: 5.67 g of the hexanediaminedihydrochloride was mixed with 0.231 g of morpholinoethane sulfonic acidin 500 microliters of concentrated sodium hydroxide in a 50 ml screwcapped tube. The volume was brought to 9.5 mls with warm water and themixture was shaken until it was mostly dissolved. 1 g of the sodiummetabisulfite was added and dissolved, and the pH was adjusted to6.0-6.2. After the reaction proceeded for 24-72 hours, the pH wasbrought up to 8.5 for two hours, and then reduced for 7 to 30 minutes.The product was then purified over a column containing 1×40 cm dextrangel beads having an exclusion volume of about 50,000 daltons (SEPHADEX G50, Pharmacia, Piscataway, N.J.).

Haptenylation of the Signal Generating Oligomer

The transaminated signal generating moiety oligomer was haptenylatedwith either biotin or fluoroscein isothiocyanate (FITC) either before orafter linking to target recognition moiety oligomer. In either case, thebiotin (NHS-LC-biotin) or FITC was dissolved in dimethylformamide andmixed with an equal volume of the transaminated oligomer dissolved in0.1M sodium bicarbonate, pH 9.0, so that the ratio of hapten to aminogroups was at least 2. The mixture was allowed to stand at roomtemperature for 16 hours. Unreacted hapten was removed by chromatographywith dextran gel beads having an exclusion volume of about 25,000daltons (SEPHADEX G 25, Pharmacia, Inc., Piscataway, N.J.).Alternatively, the excess FITC was removed by one or two butanolextractions followed by chromatography with dextran gel beads having anexclusion volume of about 25,000 daltons (SEPHADEX G 25, Pharmacia,Inc., Piscataway, N.J.). In both cases, the purified oligomer waslyophilized and redissolved in water.

Preparation of 5' Carboxyl Oligonucleotide

5 nanomoles of phosphorylated oligonucleotide were dissolved in anaqueous solution containing tenth molar imidazole and tenth molar EDAC(100 microliter, pH 6.0) and were left 20 to 50 degrees centigrade for 1to 16 hours. The contents were passed through a gel filtration columnand to the oligonucleotide containing fractions an equal volume of fourtenth molar amino caproic acid were added. After 1-16 hours thecarboxylated oligonucleotide was isolated by gel filtration.

Preparation of 5' Amino Oligonucleotide

To a ml of solution containing 5' phosphorylated oligonucleotide,sixteen microliters of N-methyl imidazole and one mL one fourth molardiaminohexane along with 4 mg EDAC were added, the pH of the solutionwas adjusted to about 6. After an overnite reaction 5' aminooligonucleotide was isolated by gel filtration.

Preparation of Ester Linked Probes

To a ml. of aqueous solution containing 5 nanomoles each of 5' hydroxyloligonucleotide and 5' carboxyl oligonucleotide, 10 mg. of EDAC wereadded. The solutions were left at room temperature overnite afteradjusting the pH to 6. The labeled probe was isolated by chromatographywith cross-linked agarose gel beads (SEPHAROSE CL6B, Pharmacia, Inc.,Piscataway, N.J.) or beads of dextran gel cross-linked withbisacrylamide having an exclusion volume of about 200,000 daltons(SEPHACRYL S-200, Pharmacia, Inc., Piscataway, N.J.).

Preparation of Amide Linked Probes

To a ml. of aqueous solution containing 5 nanomoles of each 5' aminooligonucleotide and 5' carboxyl oligonucleotide, 10 mg. of EDAC wereadded. The solutions were left at room temperature overnite afteradjusting the pH to 6. The labeled probe was isolated by chromatographywith cross-linked agarose gel beads (SEPHAROSE CL6B, Pharmacia, Inc.,Piscataway, N.J.) or beads of dextran gel cross-linked withbisacrylamide having an exclusion volume of about 200,000 daltons(SEPHACRYL S-200, Pharmacia, Inc., Piscataway, N.J.).

Preparation of Phosphoamide and Phosphodiester Linked Probes

To a ml. of aqueous solution containing 5 nanomoles each of 5' amino or5' hydroxyl oligonucleotide and 5' phosphate oligonucleotide, 10 mg. ofEDAC were added. The solutions were left at room temperature overniteafter adjusting the pH to 6. The labeled probe was isolated bychromatography with cross-linked agarose gel beads (SEPHAROSE CL6B,Pharmacia, Inc., Piscataway, N.J.) or beads of dextran gel cross-linkedwith bisacrylamide having an exclusion volume of about 200,000 daltons(SEPHACRYL S-200, Pharmacia, Inc., Piscataway, N.J.).

Chemical Linkage of the Probe Components Using HeterobifunctionalReagents

A number of heterobifunctional reagents from commercial sources (likePierce Chemicals) are used to link the two components to form afunctional probe. Of these reagents may be mentioned Succinimidyl4-(maleimidomethyl) cyclohexane-1-carboxylate (SMCC), N-Succinimidyl3-(2-pyridyl dithio) propionate (SPDP), N-Succinimidyl (4-iodoacetyl)aminobenzoate (SIAB), Succinimidyl 4-(p-maleimidophenyl) butyrate(SMPB), and the like. These reagents are adapted to link the probes byseparate reaction of the two components with each other.

Characterization of the Product

The labeled probe was characterized in two ways. The first was bypolyacrylamide gel electrophoresis, where an increase in the molecularweight of the product was noted as evidence that the linking of theprobe to the label was successful. Secondly, the product was shown to befunctional in the assay to detect DNA from Neisseria gonorrhea. In thisassay, the biotin or FITC was detected where the probe had hybridized toNeisseria gonorrhea, indicating that the target recognition oligomer wascovalently attached to the signal generating oligomer.

What is claimed is:
 1. A chemical synthesis of a labeled nucleotideprobe comprising the steps of:a) providing a first target recognitionmoiety comprising a nucleotide sequence of at least about 15 nucleotidebases, said sequence containing at least one 5' end and 3' end, b)chemically altering said first target recognition moiety to contain areactive functionality at said 5' end, said 3' end or both, and c)providing a second signal generating moiety, having at least oneterminus containing a functionality that is capable of reacting with atleast one reactive functionality provided on said first targetrecognition moiety, and d) chemically reacting said first targetrecognition moiety now containing reactive functionality with said atleast one terminus of said second signal generating moiety, tochemically join these two moieties and produce said labeled nucleotideprobe; wherein said reactive functionality of step (b) is a carboxylgroup and said terminus of said signal generating moiety is a hydroxylgroup.
 2. A method according to claim 1 wherein said phosphorylated endis activated with EDAC and then reacted with an excess of ε-aminocaproic acid, producing a carboxyl group.
 3. A method according to claim1 wherein said signal generating moiety is labeled with a hapten.
 4. Achemical synthesis for making a labeled nucleotide probe comprising thesteps of:a) providing a first target recognition moiety comprising anucleotide sequence of at least about 15 nucleotide bases, said sequencecontaining a 5' end with a free 5' group and a 3' end with a free 3'group; b) altering said first target recognition moiety with a phosphategroup at said free 5' group of said 5' end, or said free 3' group ofsaid 3' end, or said free 5' group of said 5' end and said free 3' groupof said 3' end to form a phosphorylated target recognition moiety; c)activating the phosphate group of said phosphorylated target recognitionmoiety of step b) with imidazole and ethyl-dimethylamino-propylcarbodiimide; d) reacting said activated phosphate group of saidphosphorylated target recognition moiety of step c) with epsilon-aminocaproic acid to provide a carboxyl group at said 5' end or said 3' endof said target recognition moiety, wherein said carboxyl group is formedfrom the carboxyl group of epsilon-amino caproic acid; e) providing asecond signal generating moiety comprising a nucleic acid sequencehaving at least one terminus and a length of from about 50 to about 200bases, and further having at least one detectable label attached theretowherein said terminus contains a hydroxyl group that is capable ofreacting with said carboxyl group provided on said first targetrecognition moiety; f) chemically reacting said carboxyl group on saidfirst target recognition moiety with said hydroxyl group on said secondsignal generating moiety to covalently join said first targetrecognition moiety and said second signal generating moiety therebyproducing said labeled nucleotide probe.
 5. The chemical synthesis ofclaim 4 wherein said signal generating moiety is labeled with a hapten.6. The chemical synthesis of claim 4 wherein said hapten is biotin. 7.The chemical synthesis of claim 4 wherein said hapten is fluorescein.